近日,，中科院西雙版納熱帶植物園研究員Chuck Cannon與北京基因組所和美國得州理工大學的科研人員合作,，研發(fā)出可直接分析高通量短序列數據的程序包，簡化了高通量數據的比較基因組和轉錄組研究,。相關研究成果日前發(fā)表于《科學公共圖書館—綜合》,。
據Cannon介紹，高通量測序又稱“下一代”測序,，可一次并行對幾十萬到幾百萬條DNA分子測序,。因此，這種測序方法能對物種的轉錄組和基因組進行比以往更為全貌的分析,。
但是,，由于“下一代”測序技術原始數據的讀長只有數十或一兩百個堿基,，按照傳統(tǒng)的分析流程，必須要采取生物信息學工具將這些短的堿基數據組裝成較長的序列組或基因組框架,，才能進一步取得具有生物學意義的結果,。這制約了此類數據在沒有參照基因組的非模式生物基因組研究中的發(fā)展。
“我們研發(fā)的直接分析高通量短序列數據的程序包,，可直接通過檢測數據中kmer片段是否存在和出現頻次,，來探討一定數量目標基因組中的序列差異，所以該程序包可突破此類數據經常面臨的生物信息學的分析瓶頸,。”Cannon告訴記者,。
同時，基于先前工作,，他們還進一步改善了非組裝分析法,，比較了174個葉綠體全基因組數據，用以印證該程序包的功能和運行流程,。
該研究得到中科院知識創(chuàng)新工程重要方向項目和云南省高端科技人才引進計劃項目的資助,。(生物谷Bioon.com)
doi:10.1371/journal.pone.0048995
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Reference-Free Comparative Genomics of 174 Chloroplasts
Chai-Shian Kua, Jue Ruan, John Harting, Cheng-Xi Ye, Matthew R. Helmus, Jun Yu, Charles H. Cannon
Direct analysis of unassembled genomic data could greatly increase the power of short read DNA sequencing technologies and allow comparative genomics of organisms without a completed reference available. Here, we compare 174 chloroplasts by analyzing the taxanomic distribution of short kmers across genomes [1]. We then assemble de novo contigs centered on informative variation. The localized de novo contigs can be separated into two major classes: tip = unique to a single genome and group = shared by a subset of genomes. Prior to assembly, we found that ~18% of the chloroplast was duplicated in the inverted repeat (IR) region across a four-fold difference in genome sizes, from a highly reduced parasitic orchid [2] to a massive algal chloroplast [3], including gnetophytes [4] and cycads [5]. The conservation of this ratio between single copy and duplicated sequence was basal among green plants, independent of photosynthesis and mechanism of genome size change, and different in gymnosperms and lower plants. Major lineages in the angiosperm clade differed in the pattern of shared kmers and de novo contigs. For example, parasitic plants demonstrated an expected accelerated overall rate of evolution, while the hemi-parasitic genomes contained a great deal more novel sequence than holo-parasitic plants, suggesting different mechanisms at different stages of genomic contraction. Additionally, the legumes are diverging more quickly and in different ways than other major families. Small duplicated fragments of the rrn23 genes were deeply conserved among seed plants, including among several species without the IR regions, indicating a crucial functional role of this duplication. Localized de novo assembly of informative kmers greatly reduces the complexity of large comparative analyses by confining the analysis to a small partition of data and genomes relevant to the specific question, allowing direct analysis of next-gen sequence data from previously unstudied genomes and rapid discovery of informative candidate regions.
